Install TopHat

[chengeng]

Hi,all
I am a novel user .I have downloaded the tophat software and wanted to use it to deal with some RNA sequences,but failed to install tophat.I want to know what I need to do before installing the tophat,thanks.

all the best,
Geng Chen

[ECO]

Hey chengeng,

Anyone who may be able to help would probably want to know what type of operating system you are using, what commands you tried, and what the failures were.

[iloveneworleans]

1) To use TopHat, you will need the following Bowtie in your PATH:
* bowtie
* bowtie-inspect
* bowtie-build
In other words, you need to install Bowtie firstly and copy the above 3 files to /usr/local/bin.
2) You will also need Python version 2.4 or higher.
You can download Python from the below link:

http://www.python.org/download/

3) To install TopHat, unpack the tarball and change to the package directory as follows:
tar zxvf tophat-1.0.7.tar.gz
cd tophat-1.0.7/
Now build the package:
./configure --prefix=/path/to/install/directory/
make
Finally, install TopHat:
make install
4) Go to the Tophat/bin and copy all files to /usr/local/bin;
5) Finally, you can run Tophat.

[chengeng]

Problems

Hey chengeng,

Anyone who may be able to help would probably want to know what type of operating system you are using, what commands you tried, and what the failures were.

Thanks.My operating system is fedora6.The commads I tried:./configure,but it output :
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for gawk... gawk
checking for a BSD-compatible install... /usr/bin/install -c
checking for ranlib... ranlib
checking for ar... ar
checking for perl... /usr/bin/perl
checking for bash... /bin/bash
checking for a Python interpreter with version >= 2.4... python
checking for python... /usr/bin/python
checking for python version... 2.4
checking for python platform... linux2
checking for python script directory... ${prefix}/lib/python2.4/site-packages
checking for python extension module directory... ${exec_prefix}/lib/python2.4/site-packages
checking if gcc accepts -m64... yes
checking for gzread in -lz... no
checking how to run the C++ preprocessor... g++ -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... no
checking for sys/types.h... no
checking for sys/stat.h... no
checking for stdlib.h... no
checking for string.h... no
checking for memory.h... no
checking for strings.h... no
checking for inttypes.h... no
checking for stdint.h... no
checking for unistd.h... no
checking for stdlib.h... (cached) no
checking for string.h... (cached) no
checking for unistd.h... (cached) no
checking for stdbool.h that conforms to C99... no
checking for _Bool... no
checking for an ANSI C-conforming const... no
checking for int32_t... no
checking for size_t... no
checking for uint32_t... no
checking for uint64_t... no
checking for uint8_t... no
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... unknown
checking for _LARGE_FILES value needed for large files... unknown
checking for stdlib.h... (cached) no
checking for GNU libc compatible malloc... no
checking for memset... no
checking for strdup... no
checking for strrchr... no
checking for strtol... no
checking for strsep... no
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking whether make sets $(MAKE)... yes
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking dependency style of g++... gcc3
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: executing depfiles commands
what I need to do to intall tophat successfully?thans very much.

[chengeng]

1) To use TopHat, you will need the following Bowtie in your PATH:
* bowtie
* bowtie-inspect
* bowtie-build
In other words, you need to install Bowtie firstly and copy the above 3 files to /usr/local/bin.
2) You will also need Python version 2.4 or higher.
You can download Python from the below link:

http://www.python.org/download/

3) To install TopHat, unpack the tarball and change to the package directory as follows:
tar zxvf tophat-1.0.7.tar.gz
cd tophat-1.0.7/
Now build the package:
./configure --prefix=/path/to/install/directory/
make
Finally, install TopHat:
make install
4) Go to the Tophat/bin and copy all files to /usr/local/bin;
5) Finally, you can run Tophat.

Thanks.I was tried these commands before,but can not compile successfully.

[Cole Trapnell]

The configure script is answering "no" to an awful lot of questions about the gcc installation. Which version of gcc do you have, and did you install it via fedora's package manager?

[chengeng]

The configure script is answering "no" to an awful lot of questions about the gcc installation. Which version of gcc do you have, and did you install it via fedora's package manager?

Thank you very much.The version of gcc which I use is 4.1.1 20061011 (Red Hat 4.1.1-30).Yes,I was installed it via the fedora's package manager,but failed to install it.I don know why?

[Cole Trapnell]

Can you tell us what compile errors appear when you try "make install"?

[yifangt]

problem with tophat installation

Still struggle with the installation of tophat-1.2.0.
I have tried everything suggested above, but still not through!
Only one thing I was not sure is the PATH settings. Here is what I did:
1. bowtie was successfully installed in $HOME/Downloads/bowtie-0.12.7, and it was running correctly with my real data;
2. samtools was also downloaded and installed in $HOME/Downlads/samtools-0.1.13. At least no complain was seen during installation.
3. tarball of tophat-1.2.0 was downloaded and extracted in $HOME/Downloads/tophat-1.2.0.
4. the libraries needed was copied in other folders created by:

cp $HOME/Downloads/samtools-0.1.8/libbam.a $HOME/software/bin/lib
cp $HOME/Downloads/samtools-0.1.8/*.h $HOME/software/bin/include/bam

By the way, I have added following lines to my /etc/bash.bashrc:

export PATH=$PATH:$HOME/Downloads/samtools-0.1.13
export PATH=$PATH:$HOME/Downloads/software/bin/lib:$HOME/software/bin/lib/include/bam

4. Then I went to tophat-1.2.0 and issued:

./configure --prefix=$HOME/Downloads/tophat-1.2.0 --with-bam=$HOME/software/bin

No complain.

......
config.status: creating config.h
config.status: executing depfiles commands

-- tophat 1.2.0 Configuration Results --
  C compiler:          gcc -Wall -m64 -O3  -DNDEBUG
  C++ compiler:        g++ -Wall -m64 -O3  -DNDEBUG -I/home/yifang/software/bin/include
  GCC version:         gcc (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5
  Host System type:    x86_64-unknown-linux-gnu
  Install prefix:      /home/yifang/Downloads/tophat-1.2.0
  Install eprefix:     ${prefix}

  See config.h for further configuration information.
  Email <[email protected]> with questions and bug reports.

5. but the error showed up when try to make by:
:~/Downloads/tophat-1.2.0$ make

---------------------error message---------------------
make  all-recursive
make[1]: Entering directory `/home/yifang/Downloads/tophat-1.2.0'
Making all in src
make[2]: Entering directory `/home/yifang/Downloads/tophat-1.2.0/src'
..
juncs_db.cpp:327:   instantiated from here
./SeqAn-1.1/seqan/sequence/string_base.h:207: error: no matching function for call to ‘_setLength(seqan::String<char, seqan::CStyle>&, int)’
make[2]: *** [juncs_db.o] Error 1
make[2]: Leaving directory `/home/yifang/Downloads/tophat-1.2.0/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/yifang/Downloads/tophat-1.2.0'
make: *** [all] Error 2

Believe is the setting problem. Please help me out this. Thanks a lot!

[ttnguyen]

Sounds like the Seqan problem that I and someone met before. This way worked for me:

http://seqanswers.com/forums/showthread.php?p=33825#post33825

[yifangt]

top-hat installation solved!

Yes, following ttnguyen's link and found out the problem IS the Seqan folder.
Download the new version Seqan-1.2 (Did not try version 1.3 yet), unzip and copy replace the same folder in tophat-1.2.0/src/SeqAn-1.1/
then do the configuration->make->make install as I listed above. It is working now! Thanks ttnguyen!

[Wei-HD]

Hi all,

I have used the new version Seqman -1.2, but I still had error when I try to make:

/configure --prefix=/usr/local/bin --with-bam=/Users/wei/desktop/a

-- tophat 1.2.0 Configuration Results --
C compiler: gcc -Wall -arch x86_64 -O3 -DNDEBUG
C++ compiler: g++ -Wall -arch x86_64 -O3 -DNDEBUG -I/Users/wei/desktop/a/include
GCC version: i686-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 (Apple Inc. build 5493)
Host System type: i386-apple-darwin9.8.0
Install prefix: /usr/local/bin
Install eprefix: ${prefix}

See config.h for further configuration information.
Email <[email protected]> with questions and bug reports.

make

make all-recursive
Making all in src
g++ -Wall -arch x86_64 -O3 -DNDEBUG -I/Users/wei/desktop/a/include -I./SeqAn-1.1 -Wall -arch x86_64 -O3 -DNDEBUG -I/Users/wei/desktop/a/include -L/usr/lib -o tophat_reports -L/Users/wei/desktop/a/lib tophat_reports.o ../src/libtophat.a -lbam -lz -lz
ld warning: in /Users/wei/desktop/a/lib/libbam.a, file is not of required architecture
Undefined symbols:
"_samopen", referenced from:
driver(__sFILE*, __sFILE*, __sFILE*, __sFILE*, __sFILE*, __sFILE*, __sFILE*, __sFILE*)in tophat_reports.o
ld: symbol(s) not found
collect2: ld returned 1 exit status
make[2]: *** [tophat_reports] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2


Hopefully someone can give me some hint. Many thanks in advance!

[jdjax]

tophat configure issues

I am having issues with installing TopHat 1.3.1. I have bowtie and samtools in my path. I checked and have python 2.4. I have followed the instructions stated on the TopHat manual and I still get error.

[jadf@flseq tophat-1.3.1.Linux_x86_64]$ ./configure --prefix=/usr/local/bin/
-bash: ./configure: No such file or directory

I think that this has to be some sort of computer or env issue but I have no clue how to fix it. I would appreciate your help.

1) To use TopHat, you will need the following Bowtie in your PATH:
* bowtie
* bowtie-inspect
* bowtie-build
In other words, you need to install Bowtie firstly and copy the above 3 files to /usr/local/bin.
2) You will also need Python version 2.4 or higher.
You can download Python from the below link:

http://www.python.org/download/

3) To install TopHat, unpack the tarball and change to the package directory as follows:
tar zxvf tophat-1.0.7.tar.gz
cd tophat-1.0.7/
Now build the package:
./configure --prefix=/path/to/install/directory/
make
Finally, install TopHat:
make install
4) Go to the Tophat/bin and copy all files to /usr/local/bin;
5) Finally, you can run Tophat.

[dpryan]

You downloaded the binary

What the error message is telling you is that the "configure" script (usually the first script run to figure out how to properly compile a program) isn't in the directory from which you're typing the command. The reason is that you downloaded the binary version and are following the instructions to compile the whole thing from source code (I'm assuming you don't really want to do that, since you didn't actually download the source code).

Either copy the executables in that directory to somewhere in your $PATH or add that directory to your $PATH. Either way, that'll probably be easier than actually compiling the thing from scratch.

[arcolombo698]

I already have Tophat2 installed, but how do I just install the update, without going through the full installation?

Thank you